结合RNAi技术的三重表达HCV DNA疫苗的构建及其在HepG2细胞中的表达

目的:构建多表位抗原基因、hIL-12、小分子干扰RNA(siRNA)共质粒表达的新型复合丙型肝炎DNA疫苗并在HepG2细胞中表达.方法:设计并合成复合多表位丙肝抗原基因,将其与加强型绿色荧光蛋白(EGFP)基因融合克隆进真核表达载体pVAX1的多克隆位点中;利用pVAX1载体上卡那霉素抗性基因与复制起始位点之间的非功能区域,将带CMV启动子的hIL-12表达单元克隆进该区域的BspH Ⅰ位点中;同时将8组针对丙肝的siRNA表达单元分别克隆进载体复制起始位点下游非功能区域的Mlu Ⅰ位点上,构建三重表达的HCV DNA疫苗pVAX1-HC-EGFP-hIL12-siRNA.以该重组质粒转染人肝癌细胞系HepG2,通过EGFP的荧光标记观察多表位抗原的表达;以靶向EGFP的siRNA做为对照验证siRNA的表达及其干扰效果;ELISA测定培养细胞上清中hIL-12的表达.结果:经酶切鉴定和测序证实三重表达的复合HCV DNA疫苗构建成功.在转染细胞中检测到绿色荧光,证实抗原表达;靶向EGFP的siRNA亦能显著抑制EGFP的表达;转染后48 h hIL-12的检出量为1 289 ng/L细胞上清,72 h检出量为1 712 ng/L细胞上清.结论:成功地构建多表位抗原基因、hIL-12和siRNA共质粒表达的丙肝DNA疫苗,并能在真核细胞中有效表达抗原基因、hIL-12并介导RNA干扰效应.为进一步研究该DNA疫苗抗HCV的免疫治疗和基因治疗效果打下基础.     

一个RNA剪接调控元件分类方法的研究

序列分类方法被广泛应用于各种生物信息学问题,例如转录调控元件识别和蛋白结构预测。本研究设计了一个新的基于序列特征的分类方法,并将其用于RNA剪接调控元件的研究。该方法从已知剪接元件中抽取序列特征,构建一个打分算法,由此预测未知元件RNA剪接调控功能。作为应用实例,采用已知外显子剪接增强子和沉默子(ESE和ESS)八联体作为实验数据,对本方法和若干已知常用方法的预测结果进行比较,3类计算验证实验中的平均预测精度为93%,表现出良好预测精度,且其透明的预测结构可帮助进行生物解释。该研究提供了一种可用于分析生物序列数据的新方法,给出了一个从生物信息学角度来研究基因调控问题的新途径。     

人源性抗HFRS病毒抗体基因真核表达载体的构建及鉴定

构建人源性抗ＨＦＲＳ病毒基因工程抗体基因的表达载体,为其进一步在真核细胞中表达奠定基础。方法：经多次克隆将人源性抗ＨＦＲＳ病毒抗体可变区基因与启动子,增强子、前导肽序列和剪接供体信号等真有达元件及人抗体恒定区基因和抗生素选标记基因相连接。     

肝癌细胞中HLA Ⅰ类重链基因表达与启动子区域甲基化的相关性

目的： 研究肝癌细胞株中DNA甲基化与HLA Ⅰ类分子异常表达的相关性.方法： 应用MSP技术对相关细胞系的HLA I类分子重链A、B、C位点启动子区域CpG岛的甲基化状态进行分析, Real-time PCR检测HLA Ⅰ类分子重链mRNA水平的表达情况, Western blot检测RNA干扰后HLA Ⅰ类分子重链表达情况.结果： 在8株肝癌细胞系中HLA I类分子重链A、C位点启动子区域CpG岛存在甲基化; 将启动子区域的DNA甲基化与相关基因表达数据相比较显示二者没有关联性; 在RNA干扰DNA甲基化转移酶3a或3b的肝癌细胞系SMMC7721中, 比较基因干扰前后HLA Ⅰ类分子重链蛋白表达无显著变化.结论： 在研究的肝癌细胞系中DNA甲基化没有参与调控肝癌中HLA Ⅰ类分子的异常表达.     

降钙素/降钙素基因相关肽基因前体RNA的加工

降钙素和降钙素基因相关肽是由一个基因表达出的两种功能完全不同的多肽激素,其基因的表达主要在RNA水平上受到调控。前体RNA在加工成为成熟RNA的过程中,在不同的组织中经过不同的剪接形成不同的RNA。其剪接的特异性受到顺式元件和反式因子的调控,基因 的exon4上游剪接受点和下游polyA位点均存在弱的加工位点,通过增强子序列使之产生选择性剪接,另外,可能存在组织特异的反式剪接因子。     

小鼠Ii分子的克隆表达及在COS-7细胞中的亚细胞定位

目的 获取BALB／c小鼠Ii链编码基因，构建真核表达载体并在真核细胞中表达。方法 RT-PCR获取BALB／c小鼠Ii链编码基因，插入pEGFP真核表达载体，脂质体转染COS-7细胞，荧光显微镜和激光共聚焦观察外源基因的表达。结果 外源基因在COS-7细胞中得到高效表达，激光共聚焦的结果显示，外源基因定位在细胞的内膜系统，并能够和I-A^d分子形成聚集体。结论 Ii链在真核细胞中表达后定位在细胞的内膜系统并能和I-Ad分子形成聚集体。     

一个新的COL4A5基因的剪接位点突变引起Alport综合征

目的 对一个Alport综合征家系进行研究,期望找到导致该家系发病的遗传基础.方法 对家系成员采样并提取DNA,对家系中的先证者和1名正常对照进行COL4A5基因全部编码区域的突变检测,限制性片段长度多态件分析技术对家系中所有成员和200名正常对照进行验证.结果 在该Alport综合征家系中发现一个新的COL4A5基因的剪接位点突变c.1517-1G＞T,而在家系的未患病成员,以及对照人群中未能检测到该突变.结论 发现了一个新的COL4A5基因的剪接位点改变c.1517-IG＞T,该突变可导致Alport综合征,该发现丰富了引起Alport综合征的COL4A5基因的突变谱.     

一例德朗热综合征患儿的致病基因变异分析

目的对1例疑诊德朗热综合征(Cornelia de Lange syndrome,CdLS)的患儿进行致病基因变异检测,明确其发病原因。方法应用高通量捕获测序对CdLS相关致病基因(NIPBL、SMC1A、SMC3、RAD21和HDAC8)进行测序,用Sanger测序验证测序结果以及致病基因的家系分析。结果患儿NIPBL基因存在c.6109-1G>A杂合剪接变异,Sanger测序验证结果表明患儿父母均未携带此变异,提示为新发变异,该变异未在HGMD及ExAC数据库收录。根据Human Splicing Finder预测剪接软件,预测该剪接变异将改变NIPBL基因剪接位点,为致病性变异。未发现SMC1A、SMC3、RAD21和HDAC8基因致病性变异。结论NIPBL基因c.6109-1G>A剪接变异可能是该例患儿的发病原因,新变异的检出丰富了NIPBL基因变异谱。     

与剪接、翻译偶联的PTC-mRNA NMD降解机制

最新研究发现 ,真核细胞前体 m RNA剪接不仅仅是前体 m RNA的加工步骤 ,而且在翻译过程中也起到重要的监控作用。通过剪接 ,外显子 -外显子连接点复合物结合于 m RNA剪接位点上游 2 0 bp处。如果 m RNA剪接位点上游大于 5 0～ 5 5 bp处出现无义突变 ,则这种翻译提前终止密码子 m RNA将会在最后的翻译过程中通过外显子 -外显子连接点复合物、Upf蛋白以及帽结合蛋白之间的相互作用 ,被引入脱帽、降解过程     

GLI3基因在单纯性马蹄内翻足发生中的调控机制

目的 探讨在单纯性马蹄内翻足发生过程中GLI3基因的凋控机制.方法 构建荧光素酶报告基因表达载体,分析大鼠Gli3基因5′侧翼启动子区域的活性.用P-Match软件预测Gli3基因上游序列中转录因子的结合位点,并通过染色质免疫沉淀实验、凝胶迁移实验验证.用RNA干扰实验以及构建Hoxd13表达载体,观察其在L6细胞中对Gli3基因表达的影响.结果 在大鼠Gli3基因序列的启动子区域发现2个Hoxd13的结合位点,染色质免疫沉淀和凝胶迁移实验证实Hoxd13结合于结合位点2上.Hoxd13表达下调时,Gli3基因表达明显上调.Hoxd13基因表达上调时,Gli3基因则表达下调.结论 在大鼠胚胎肢体发育中,Hoxd13蛋白可能与Gli3基因启动子区的Hoxd13结合位点2结合,调控Gli3的表达.     

Processing of fish Ig heavy chain transcripts: diverse splicing patterns and unusual nonsense mediated decay

While the diversification of the antigen-binding sites is realized by genomic VDJ rearrangements during B cell differentiation, different forms of immunoglobulin (Ig) heavy (H) chains can be produced through multiple splicing pathways. In most vertebrates, the secreted (S) and membrane (Mb) forms of IgM chain are created by alternative splicing through usage of a cryptic splice site in Cμ4 allowing the junction to the TM exon. The processing pattern for Igμ is different in teleosts, which generally use the Cμ3 donor site instead. In ancient fish lineages, multiple unusual splicing patterns were found for Ig H chain, involving donor sites that do not always follow the classical consensus. The production of IgD versus IgM H chains seems to be generally realized by alternative splicing in all vertebrates, but typical teleost IgD H chains are chimeric and contains a Cμ1 domain. Together, these observations raise questions on how different fish regulate RNA splicing and if their splicing machinery is especially complex. A preliminary scan of the zebrafish and stickleback genomes provides evidence that gene orthologs to the mammalian main splice factors are highly conserved as single copy genes, while the snRNPs U repertoire may be different and may explain other particular features of RNA processing in fish.     

Predicting the impact of single nucleotide variants on splicing via sequence‐based deep neural networks and genomic features

Single nucleotide mutations in exonic regions can significantly affect gene function through a disruption of splicing, and various computational methods have been developed to predict the splicing‐related effects of a single nucleotide mutation. We implemented a new method using ensemble learning that combines two types of predictive models: (a) base sequence‐based deep neural networks (DNNs) and (b) machine learning models based on genomic attributes. This method was applied to the Massively Parallel Splicing Assay challenge of the Fifth Critical Assessment of Genome Interpretation, in which challenge participants predicted various experimentally‐defined exonic splicing mutations, and achieved a promising result. We successfully revealed that combining different predictive models based upon the stacked generalization method led to significant improvement in prediction performance. In addition, whereas most of the genomic features adopted in constructing machine learning models were previously reported, feature values generated with DSSP, a DNN‐based splice site prediction tool, were novel and helpful for the prediction. Learning the sequence patterns associated with normal splicing and the change in splicing site probabilities caused by a mutation was presumed to be helpful in predicting splicing disruption.     

Sequence-specific flexibility organization of splicing flanking sequence and prediction of splice sites in the human genome

More and more reported results of nucleosome positioning and histone modifications showed that DNA structure play a well-established role in splicing. In this study, a set of DNA geometric flexibility parameters originated from molecular dynamics (MD) simulations were introduced to discuss the structure organization around splice sites at the DNA level. The obtained profiles of specific flexibility/stiffness around splice sites indicated that the DNA physical-geometry deformation could be used as an alternative way to describe the splicing junction region. In combination with structural flexibility as discriminatory parameter, we developed a hybrid computational model for predicting potential splicing sites. And the better prediction performance was achieved when the benchmark dataset evaluated. Our results showed that the mechanical deformability character of a splice junction is closely correlated with both the splice site strength and structural information in its flanking sequences.     

Genome-wide identification of spliced introns using a tiling microarray

The prediction of gene models from genome sequence remains an unsolved problem. One hallmark of eukaryotic gene structure is the presence of introns, which are spliced out of pre-mRNAs prior to translation. The excised introns are released in the form of lariats, which must be debranched prior to their turnover. In the yeast Saccharomyces cerevisiae, the absence of the debranching enzyme causes these lariat RNAs to accumulate. This accumulation allows a comparison of tiling array signals of RNA from the debranching mutant to the wild-type parent strain, and thus the identification of lariats on a genome-wide scale. This approach identified 141 of 272 known introns, confirmed three previously predicted introns, predicted four novel introns (of which two were experimentally confirmed), and led to the reannotation of four others. In many instances, signals from the tiling array delineated the 5' splice site and branchpoint site, confirming predicted gene structures. Nearly all introns that went undetected are present in mRNAs expressed at low levels. Overall, 97% of the significant probes could be attributed either to spliced introns or to genes up-regulated by deletion of the debranching enzyme. Because the debranching enzyme is conserved among eukaryotes, this approach could be generally applicable for the annotation of eukaryotic genes and the detection of novel and alternative splice forms.     

Homologies between small nuclear RNAs and LAV/HTLV-III sequences and their possible role in the cytopathic effect of the virus

The mechanism of action of LAV/HTLV-III resulting in a pronounced cytopathic effect is still unknown. We demonstrate that the long terminal repeat (LTR) sequence and env gene of LAV/HTLV-III contain regions of 70-80% homology and/or complementarity with regions of small nuclear (sn) RNAs U1 and U2. On this basis, we hypothesize that the cytotoxic effect of LAV/HTLV-III is due - at least partly - to the inhibition of processing of cellular hnRNAs by competing for splice junction sites and/or by complexing with U1 and especially U2 RNAs.     

非小细胞肺癌影像学特征与基因表达间相关性的探索性研究

影像基因组学通过挖掘肿瘤的影像和基因组学间的关联性,将两者的优势互补,以此指导不同患者个体化治疗方案的制定、预后评估、疗效检测等。针对非小细胞肺癌(NSCLC),建立其CT影像定量特征与基因表达之间的映射。首先,将对应的CT影像中肿瘤区域进行分割和特征提取,选用66种三维定量特征作为肿瘤区域影像特征集;然后,利用基因组学数据分析流程,在原始基因数据经过预处理、聚类后,获取其第一主成分作为具有相似表达谱基因聚类结果的代表;最后,运用基因芯片显著性分析算法探寻两者之间的相关性,并进行基因集的富集分析和预测模型的建立。对癌症图像归档数据库(TCIA)中的26例NSCLC影像数据和基因表达综合数据库(GEO)中相对应的基因数据进行分析,共得到126组成对的显著关联(q<0.05)。将所得结果中的29组元基因建立预测模型,并通过TCIA中更新的211组数据,对其中10组预测准确率大于70%且预测的元基因有生物学意义的预测模型进行验证,最终预测准确率为35.48%～80.85%,10个预测模型中有6个的准确率在70%以上。实验结果表明,特定的影像特征或其组合可以作为基因表达的影像标记物。